The purpose of this model is to understand how genetic architectures of alternative reproductive tactics impact their maintenance in populations. I’m using an individual-based simulation model with different selection scenarios, types of alternative tactics, and genetic architectures (genome-wide additive genetic variance, supergenes, expression networks).

Overview of the model

Males can be courters or not-courters and parents or not-parents. When the model is run with both traits, this results in four possible morphs: courter/parent, courter/not-parent, not-courter/parent, and not-courter/not-parent. Generations are non-overlapping and there is one reproductive bout per generation. In each generation, the population follows the following timeline:

1. Choosing a nest

A female samples 50 males and chooses a male to nest with based on his courtship trait. If there are no courtship traits in the model, she chooses based on the male’s parental trait. If she does not encouter an acceptable male, she does not nest. If she encounters multiple equally-acceptable males, she randomly selects one of them.

2. Fertilization

Once a female decides to nest, up to three males can fertilize the nest. Courters and parental males can contribute more sperm than non-courter and non-parental males: \(r_{courter}=r_{parent}=8\) and \(r_{non-courter}=r_{non-parent}=4\). A courter/non-parent has \(r_{non-parent}\) and a non-courter/parent has \(r_{parent}\). The male with whom the female is nesting gets \(r_{parent}/\Sigma{n_{sperm}}\) and additional non-parental males (up to 2) get \((r_{non-parent}*0.5/\Sigma{n_{sperm}})\), where \(\Sigma{n_{sperm}}\) is the total number of sperm contributed by all of the males, weighted by the sperm competition factor (0.5 is the default for all males except the nesting male). So, when a female mates with one courter and two non-parentals, \(\Sigma{n_{sperm}}\) = \(r_{courter}\) + 2\(*\)(0.5\(*\)\(r_{sneaker}\)), where \(r_{courter}\) = 8 and \(r_{sneaker}\) = 4, therefore \(\Sigma{n_{sperm}}\) = 12.

That being said, every time a male mates he uses his sperm, so after one mating where a courter fertilizes 50% of the female’s 4 eggs, he only has 6 sperm for his next mating.

3. Nest Survival

Before the babies can survive, the nest has to survive. This step is only relevant when parental traits are in the model - if only the courtship trait is specified, then all progeny in the nest survive at this point. When males have the parental trait, if the female has given eggs to a non-parental male (because she chose based on courtship traits), then the nest has a 10% chance of surviving. If the female has given eggs to a parental male, the nest has a 90% chance of surviving.

4. Density-dependent survival

Once the identities of the surviving nests are known–along with the identities of the parents, including sneaker parents–the offspring are created in the simulation. The offspring are created to fill the full carrying capacity of the population, with the numbers per nest being equally divided among all surviving offspring. This allows the population to maintain a constant population size (prior to viability selection) while maintaining the relative successes of the given genotypes/morphs.

5. Viability selection

Before becoming adults, the offspring experience viability selection. Courters and parental males are disfavored in viability selection, with a survival probability of 0.9950125. If an individual is both a courter and a parental male, the survival probability is 0.9900498. Non-courters and non-parental males have survival probabilities of 1.

Evaluating equilibrium

After 10000 generations, I begin tracking the change in frequency of the courter and parent traits, and do so for 2000 additional generations. I calculate the variance in the change in frequency over those 2000 generations. I declare an equilibrium (‘stasis’) has been reached if the last change in frequency of both traits is less than the variance in changes in frequency.

Unlinked additive genetic variance

In these cases, the traits are encoded by a number (50) of loci, whose alleles contribute additively to determine the trait value. These alleles are all freely recombining and are not adhered to any physical genomic location (aka this is a classical quantitative genetics approach). The overall trait value is compared to a population-level threshold (which is static, in these cases), and if the trait value is above the threshold the male takes the parent or courter morph and if it is below he does not. Below, I’m showing the results from 10 replicates of each scenario.

Courter trait

Females choose nests based on whether the male is a courter or not, and they all prefer courters all of the time (the female preference does not have a genetic basis and does not evolve). The only way that non-courters produce offspring is through sneaking, but all males can be sneakers (both courters and non-courters). Because parental care is not incorporated in this model, all nests survive.

Frequency of the courter morph (each color represents a different replicate)

Frequency of the courter morph (each color represents a different replicate)

Of the 20 replicates, 0 reached an equilibrium by 10000 generations.

Frequency of courters in final generation
CourterFreq CourterW NonCourterW
courter_unlinked_1_summary.txt_1 1 2.00401 0
courter_unlinked_1_summary.txt_2 1 2.08333 0
courter_unlinked_1_summary.txt_3 1 2.11416 0
courter_unlinked_1_summary.txt_4 1 1.97628 0
courter_unlinked_2_summary.txt_1 1 2.00401 0
courter_unlinked_2_summary.txt_2 1 2.08333 0
courter_unlinked_2_summary.txt_3 1 2.11416 0
courter_unlinked_2_summary.txt_4 1 1.97628 0
courter_unlinked_3_summary.txt_1 1 1.94175 0
courter_unlinked_3_summary.txt_2 1 2.02840 0
courter_unlinked_3_summary.txt_3 1 2.10526 0
courter_unlinked_3_summary.txt_4 1 1.98413 0
courter_unlinked_4_summary.txt_1 1 1.94175 0
courter_unlinked_4_summary.txt_2 1 2.02840 0
courter_unlinked_4_summary.txt_3 1 2.10526 0
courter_unlinked_4_summary.txt_4 1 1.98413 0
courter_unlinked_5_summary.txt_1 1 1.93050 0
courter_unlinked_5_summary.txt_2 1 2.00401 0
courter_unlinked_5_summary.txt_3 1 1.93424 0
courter_unlinked_5_summary.txt_4 1 2.00000 0

Parental trait

All females nest with parental males, so the only way non-parental males reproduce is through sneaking. Parental males provide care that allows nests to have a 90% chance of survival. The female preference does not have a genetic basis and does not evolve.

Frequency of parent morph (each color represents a different replicate)

Frequency of parent morph (each color represents a different replicate)

Frequency of parents in final generation
ParentFreq ParentW NonParentW
parent_unlinked_1_summary.txt_1 0.514170 1.35573 0.348548
parent_unlinked_1_summary.txt_2 0.551257 1.44912 0.370690
parent_unlinked_1_summary.txt_3 0.532803 1.39179 0.344681
parent_unlinked_1_summary.txt_4 0.491429 1.37209 0.318352
parent_unlinked_2_summary.txt_1 0.514170 1.35573 0.348548
parent_unlinked_2_summary.txt_2 0.551257 1.44912 0.370690
parent_unlinked_2_summary.txt_3 0.532803 1.39179 0.344681
parent_unlinked_2_summary.txt_4 0.491429 1.37209 0.318352
parent_unlinked_3_summary.txt_1 0.552632 1.36264 0.312217
parent_unlinked_3_summary.txt_2 0.599589 1.49315 0.307692
parent_unlinked_3_summary.txt_3 0.566390 1.39927 0.282297
parent_unlinked_3_summary.txt_4 0.632609 1.75601 0.449704
parent_unlinked_4_summary.txt_1 0.552632 1.36264 0.312217
parent_unlinked_4_summary.txt_2 0.599589 1.49315 0.307692
parent_unlinked_4_summary.txt_3 0.566390 1.39927 0.282297
parent_unlinked_4_summary.txt_4 0.632609 1.75601 0.449704
parent_unlinked_5_summary.txt_1 0.548807 1.62451 0.504808
parent_unlinked_5_summary.txt_2 0.512195 1.60714 0.279167
parent_unlinked_5_summary.txt_3 0.646939 1.66246 0.404624
parent_unlinked_5_summary.txt_4 0.537223 1.25468 0.395652

Variation was maintained in 20 of the 20. 0 of the 20 populations crashed, though. Of the 20 replicates, 20 reached an equilibrium by 10000 generations.

Courtship and Parental Traits

Females choose nests based on males’ courtship trait (they all only nest with courting males, and the female preference does not have a genetic basis and does not evolve), and then the survival of the nest depends on whether the courting male is also a parental male. If the chosen male is a parental male, the nest has a 90% chance of survival. Otherwise, it only has a 10% chance. Non-courters only reproduce through sneaking.

The different runs have different outcomes.

Let’s look at the morph frequencies.

Frequency of the 4 morphs in each rep

Frequency of the 4 morphs in each rep

In some of the runs the population crashed after few generations. This is obvious when looking at the the final frequencies in a table as well:

Frequency of morphs in final generation
Generation Pop PopSize NumMal NumFem NumProgeny ParentThresh ParentFreq ParentW NonParentW CourterThresh CourterFreq CourterW NonCourterW FreqNcNp FreqCNp FreqNcP FreqCP PrefThresh PrefFreq
parent-courter_unlinked_1_summary.txt_1 11999 Pop0 997 492 505 1000 -0.0974451 0.930894 1.83188 1.705880 0.270693 0.930894 1.831880 1.70588 0.0691057 0.000000 0.000000 0.930894 NA NA
parent-courter_unlinked_1_summary.txt_2 11999 Pop1 967 461 506 1000 -0.0974451 0.911063 1.95238 1.512200 0.270693 0.911063 1.952380 1.51220 0.0889371 0.000000 0.000000 0.911063 NA NA
parent-courter_unlinked_1_summary.txt_3 11999 Pop2 946 498 448 1000 -0.0974451 0.905622 1.86475 1.297870 0.270693 0.905622 1.864750 1.29787 0.0943775 0.000000 0.000000 0.905622 NA NA
parent-courter_unlinked_1_summary.txt_4 11999 Pop3 963 463 500 1000 -0.0974451 0.902808 2.01675 1.377780 0.270693 0.902808 2.016750 1.37778 0.0971922 0.000000 0.000000 0.902808 NA NA
parent-courter_unlinked_2_summary.txt_1 11999 Pop0 997 492 505 1000 -0.0974451 0.930894 1.83188 1.705880 0.270693 0.930894 1.831880 1.70588 0.0691057 0.000000 0.000000 0.930894 NA NA
parent-courter_unlinked_2_summary.txt_2 11999 Pop1 967 461 506 1000 -0.0974451 0.911063 1.95238 1.512200 0.270693 0.911063 1.952380 1.51220 0.0889371 0.000000 0.000000 0.911063 NA NA
parent-courter_unlinked_2_summary.txt_3 11999 Pop2 946 498 448 1000 -0.0974451 0.905622 1.86475 1.297870 0.270693 0.905622 1.864750 1.29787 0.0943775 0.000000 0.000000 0.905622 NA NA
parent-courter_unlinked_2_summary.txt_4 11999 Pop3 963 463 500 1000 -0.0974451 0.902808 2.01675 1.377780 0.270693 0.902808 2.016750 1.37778 0.0971922 0.000000 0.000000 0.902808 NA NA
parent-courter_unlinked_3_summary.txt_1 11999 Pop0 955 472 483 1000 0.6239620 0.957627 1.90708 2.350000 -1.050790 0.957627 1.907080 2.35000 0.0423729 0.000000 0.000000 0.957627 NA NA
parent-courter_unlinked_3_summary.txt_2 11999 Pop1 949 473 476 1000 0.6239620 0.942918 1.90135 1.814810 -1.050790 0.942918 1.901350 1.81481 0.0570825 0.000000 0.000000 0.942918 NA NA
parent-courter_unlinked_3_summary.txt_3 11999 Pop2 948 489 459 1000 0.6239620 0.926380 1.84989 1.583330 -1.050790 0.926380 1.849890 1.58333 0.0736196 0.000000 0.000000 0.926380 NA NA
parent-courter_unlinked_3_summary.txt_4 11999 Pop3 952 490 462 1000 0.6239620 0.944898 1.79698 1.962960 -1.050790 0.944898 1.796980 1.96296 0.0551020 0.000000 0.000000 0.944898 NA NA
parent-courter_unlinked_4_summary.txt_1 11999 Pop0 955 472 483 1000 0.6239620 0.957627 1.90708 2.350000 -1.050790 0.957627 1.907080 2.35000 0.0423729 0.000000 0.000000 0.957627 NA NA
parent-courter_unlinked_4_summary.txt_2 11999 Pop1 949 473 476 1000 0.6239620 0.942918 1.90135 1.814810 -1.050790 0.942918 1.901350 1.81481 0.0570825 0.000000 0.000000 0.942918 NA NA
parent-courter_unlinked_4_summary.txt_3 11999 Pop2 948 489 459 1000 0.6239620 0.926380 1.84989 1.583330 -1.050790 0.926380 1.849890 1.58333 0.0736196 0.000000 0.000000 0.926380 NA NA
parent-courter_unlinked_4_summary.txt_4 11999 Pop3 952 490 462 1000 0.6239620 0.944898 1.79698 1.962960 -1.050790 0.944898 1.796980 1.96296 0.0551020 0.000000 0.000000 0.944898 NA NA
parent-courter_unlinked_5_summary.txt_1 11999 Pop0 552 242 310 576 -0.7776460 0.404959 0.00000 0.513889 -0.207521 0.595041 0.513889 0.00000 0.0000000 0.595041 0.404959 0.000000 NA NA
parent-courter_unlinked_5_summary.txt_2 11999 Pop1 753 360 393 832 -0.7776460 0.422222 0.00000 0.355769 -0.207521 0.577778 0.357488 0.00000 0.0000000 0.577778 0.422222 0.000000 NA NA
parent-courter_unlinked_5_summary.txt_3 11999 Pop2 771 382 389 942 -0.7776460 0.382199 0.00000 0.330508 -0.207521 0.617801 0.330508 0.00000 0.0000000 0.617801 0.382199 0.000000 NA NA
parent-courter_unlinked_5_summary.txt_4 11999 Pop3 802 382 420 913 -0.7776460 0.400524 0.00000 0.327511 -0.207521 0.599476 0.327511 0.00000 0.0000000 0.599476 0.400524 0.000000 NA NA

Multiple morphs are maintained in 20 of the 20 replicates, and those morphs contain either a parent or a courter. However, 0 of those reps with variation actually crashed.

Linked additive genetic variance

Courter trait

Frequency of the courter morph with linked QTLs (each color represents a different replicate)

Frequency of the courter morph with linked QTLs (each color represents a different replicate)

Of the 20 replicates, 0 reached an equilibrium by 10000 generations.

Frequency of courters with linked QTLs in final generation
CourterFreq CourterW NonCourterW
courter_linked_1_summary.txt_1 1 1.96850 0
courter_linked_1_summary.txt_2 1 2.04082 0
courter_linked_1_summary.txt_3 1 1.96078 0
courter_linked_1_summary.txt_4 1 2.20751 0
courter_linked_2_summary.txt_1 1 1.96850 0
courter_linked_2_summary.txt_2 1 2.04082 0
courter_linked_2_summary.txt_3 1 1.96078 0
courter_linked_2_summary.txt_4 1 2.20751 0
courter_linked_3_summary.txt_1 1 1.98807 0
courter_linked_3_summary.txt_2 1 2.02429 0
courter_linked_3_summary.txt_3 1 1.95695 0
courter_linked_3_summary.txt_4 1 2.05761 0
courter_linked_4_summary.txt_1 1 1.89753 0
courter_linked_4_summary.txt_2 1 2.00401 0
courter_linked_4_summary.txt_3 1 2.01613 0
courter_linked_4_summary.txt_4 1 1.96464 0
courter_linked_5_summary.txt_1 1 1.94932 0
courter_linked_5_summary.txt_2 1 2.03666 0
courter_linked_5_summary.txt_3 1 2.03252 0
courter_linked_5_summary.txt_4 1 2.01207 0

Every rep has the courtship trait go to fixation.

Parental trait

All females nest with parental males, so the only way non-parental males reproduce is through sneaking. Parental males provide care that allows nests to have a 90% chance of survival. The female preference does not have a genetic basis and does not evolve.

Frequency of parent morph with linked QTLs (each color represents a different replicate)

Frequency of parent morph with linked QTLs (each color represents a different replicate)

Frequency of parents with linked QTLs in final generation
ParentFreq ParentW NonParentW
parent_linked_1_summary.txt_1 0.648551 1.36592 0.242268
parent_linked_1_summary.txt_2 0.831144 1.46501 0.444444
parent_linked_1_summary.txt_3 0.670020 1.58859 0.384146
parent_linked_1_summary.txt_4 0.787524 1.68812 0.614679
parent_linked_2_summary.txt_1 0.648551 1.36592 0.242268
parent_linked_2_summary.txt_2 0.831144 1.46501 0.444444
parent_linked_2_summary.txt_3 0.670020 1.58859 0.384146
parent_linked_2_summary.txt_4 0.787524 1.68812 0.614679
parent_linked_3_summary.txt_1 0.782946 1.58663 0.491071
parent_linked_3_summary.txt_2 0.855263 1.81026 0.818182
parent_linked_3_summary.txt_3 0.818533 1.52830 0.489362
parent_linked_3_summary.txt_4 0.868571 1.66228 0.608696
parent_linked_4_summary.txt_1 0.795635 1.66334 0.485437
parent_linked_4_summary.txt_2 0.831250 1.76441 0.839506
parent_linked_4_summary.txt_3 0.851240 1.64806 0.694444
parent_linked_4_summary.txt_4 0.853229 1.65138 0.733333
parent_linked_5_summary.txt_1 0.868787 1.62471 0.530303
parent_linked_5_summary.txt_2 0.886905 1.70917 0.614035
parent_linked_5_summary.txt_3 0.875494 1.64334 0.650794
parent_linked_5_summary.txt_4 0.885714 1.61720 0.816667

Variation was maintained in 20 of the 20. 0 of the 20 populations crashed, though. Of the 20 replicates, 20 reached an equilibrium by 10000 generations.

Courtship and Parental Traits

Females choose nests based on males’ courtship trait (they all only nest with courting males, and the female preference does not have a genetic basis and does not evolve), and then the survival of the nest depends on whether the courting male is also a parental male. If the chosen male is a parental male, the nest has a 90% chance of survival. Otherwise, it only has a 10% chance. Non-courters only reproduce through sneaking.

Frequency of the two morphs with linked QTLs (courter = green, parent = blue)

Frequency of the two morphs with linked QTLs (courter = green, parent = blue)

The different runs have different outcomes.

Let’s look at the morph frequencies.

Frequency of the 4 morphs in each rep with linked QTLs

Frequency of the 4 morphs in each rep with linked QTLs

In some of the runs the population crashed after few generations. This is obvious when looking at the the final frequencies in a table as well:

Frequency of morphs in final generation (linked loci)
Generation Pop PopSize NumMal NumFem NumProgeny ParentThresh ParentFreq ParentW NonParentW CourterThresh CourterFreq CourterW NonCourterW FreqNcNp FreqCNp FreqNcP FreqCP PrefThresh PrefFreq
parent-courter_linked_1_summary.txt_1 11999 Pop0 1000 514 486 1000 -0.342681 0.404669 0.0000000 0.408497 -0.810462 0.595331 0.408497 0.000000 0.0000000 0.5953310 0.4046690 0.0000000 NA NA
parent-courter_linked_1_summary.txt_2 11999 Pop1 1000 497 503 1000 -0.342681 0.416499 0.0241546 0.389655 -0.810462 0.585513 0.405498 0.000000 0.0000000 0.5835010 0.4144870 0.0020121 NA NA
parent-courter_linked_1_summary.txt_3 11999 Pop2 1000 492 508 1000 -0.342681 0.432927 0.0000000 0.365591 -0.810462 0.567073 0.365591 0.000000 0.0000000 0.5670730 0.4329270 0.0000000 NA NA
parent-courter_linked_1_summary.txt_4 11999 Pop3 1000 512 488 1000 -0.342681 0.419922 0.0000000 0.282828 -0.810462 0.580078 0.282828 0.000000 0.0000000 0.5800780 0.4199220 0.0000000 NA NA
parent-courter_linked_2_summary.txt_1 11999 Pop0 1000 516 484 1000 -1.327780 0.905039 1.7430400 1.061220 -0.817421 0.928295 1.718160 1.162160 0.0697674 0.0251938 0.0019380 0.9031010 NA NA
parent-courter_linked_2_summary.txt_2 11999 Pop1 1000 515 485 1000 -1.327780 0.914563 1.7452200 1.181820 -0.817421 0.945631 1.718690 1.321430 0.0524272 0.0330097 0.0019418 0.9126210 NA NA
parent-courter_linked_2_summary.txt_3 11999 Pop2 1000 490 510 1000 -1.327780 0.912245 1.8031300 1.069770 -0.817421 0.926531 1.784140 1.166670 0.0673469 0.0204082 0.0061224 0.9061220 NA NA
parent-courter_linked_2_summary.txt_4 11999 Pop3 1000 494 506 1000 -1.327780 0.935223 1.7835500 1.406250 -0.817421 0.949393 1.791040 1.160000 0.0425101 0.0222672 0.0080972 0.9271260 NA NA
parent-courter_linked_3_summary.txt_1 11999 Pop0 1000 516 484 1000 -1.327780 0.905039 1.7430400 1.061220 -0.817421 0.928295 1.718160 1.162160 0.0697674 0.0251938 0.0019380 0.9031010 NA NA
parent-courter_linked_3_summary.txt_2 11999 Pop1 1000 515 485 1000 -1.327780 0.914563 1.7452200 1.181820 -0.817421 0.945631 1.718690 1.321430 0.0524272 0.0330097 0.0019418 0.9126210 NA NA
parent-courter_linked_3_summary.txt_3 11999 Pop2 1000 490 510 1000 -1.327780 0.912245 1.8031300 1.069770 -0.817421 0.926531 1.784140 1.166670 0.0673469 0.0204082 0.0061224 0.9061220 NA NA
parent-courter_linked_3_summary.txt_4 11999 Pop3 1000 494 506 1000 -1.327780 0.935223 1.7835500 1.406250 -0.817421 0.949393 1.791040 1.160000 0.0425101 0.0222672 0.0080972 0.9271260 NA NA
parent-courter_linked_4_summary.txt_1 11999 Pop0 1000 499 501 1000 -0.167134 0.438878 0.0000000 0.407143 0.446920 0.559118 0.408602 0.000000 0.0020040 0.5591180 0.4388780 0.0000000 NA NA
parent-courter_linked_4_summary.txt_2 11999 Pop1 1000 514 486 1000 -0.167134 0.463035 0.0126050 0.431159 0.446920 0.535019 0.443636 0.000000 0.0038910 0.5330740 0.4610890 0.0019455 NA NA
parent-courter_linked_4_summary.txt_3 11999 Pop2 998 503 495 1000 -0.167134 0.431412 0.0000000 0.377622 0.446920 0.568588 0.377622 0.000000 0.0000000 0.5685880 0.4314120 0.0000000 NA NA
parent-courter_linked_4_summary.txt_4 11999 Pop3 1000 515 485 1000 -0.167134 0.448544 0.0000000 0.355634 0.446920 0.549515 0.356890 0.000000 0.0019418 0.5495150 0.4485440 0.0000000 NA NA
parent-courter_linked_5_summary.txt_1 11999 Pop0 1000 494 506 1000 -0.836030 0.912955 1.8226200 1.139530 0.415143 0.912955 1.840350 0.953488 0.0688259 0.0182186 0.0182186 0.8947370 NA NA
parent-courter_linked_5_summary.txt_2 11999 Pop1 1000 506 494 1000 -0.836030 0.916996 1.7629300 1.261900 0.415143 0.916996 1.771550 1.166670 0.0750988 0.0079051 0.0079051 0.9090910 NA NA
parent-courter_linked_5_summary.txt_3 11999 Pop2 1000 489 511 1000 -0.836030 0.918200 1.8775100 1.225000 0.415143 0.924335 1.876110 1.189190 0.0695297 0.0122699 0.0061350 0.9120650 NA NA
parent-courter_linked_5_summary.txt_4 11999 Pop3 1000 485 515 1000 -0.836030 0.913402 1.9074500 1.190480 0.415143 0.923711 1.899550 1.189190 0.0701031 0.0164948 0.0061856 0.9072160 NA NA

Multiple morphs are maintained in 20 of the 20 replicates, and those morphs contain either a parent or a courter. However, 0 of those reps with variation actually crashed.

Supergenes

Courter trait

Frequency of the courter morph with supergenes (each color represents a different replicate)

Frequency of the courter morph with supergenes (each color represents a different replicate)

Of the 20 replicates, 0 reached an equilibrium by 10000 generations.

Frequency of courters with supergenes in final generation
CourterFreq CourterW NonCourterW
courter_supergene_1_summary.txt_1 1 1.99203 0
courter_supergene_1_summary.txt_2 1 1.98807 0
courter_supergene_1_summary.txt_3 1 1.99203 0
courter_supergene_1_summary.txt_4 1 1.98020 0
courter_supergene_2_summary.txt_1 1 2.01613 0
courter_supergene_2_summary.txt_2 1 2.03252 0
courter_supergene_2_summary.txt_3 1 2.06612 0
courter_supergene_2_summary.txt_4 1 1.94175 0
courter_supergene_3_summary.txt_1 1 1.96464 0
courter_supergene_3_summary.txt_2 1 2.07900 0
courter_supergene_3_summary.txt_3 1 2.00803 0
courter_supergene_3_summary.txt_4 1 1.93050 0
courter_supergene_4_summary.txt_1 1 2.01207 0
courter_supergene_4_summary.txt_2 1 1.94932 0
courter_supergene_4_summary.txt_3 1 2.01613 0
courter_supergene_4_summary.txt_4 1 1.90114 0
courter_supergene_5_summary.txt_1 1 1.97239 0
courter_supergene_5_summary.txt_2 1 1.94175 0
courter_supergene_5_summary.txt_3 1 1.89036 0
courter_supergene_5_summary.txt_4 1 1.88679 0

Parental trait

All females nest with parental males, so the only way non-parental males reproduce is through sneaking. Parental males provide care that allows nests to have a 90% chance of survival. The female preference does not have a genetic basis and does not evolve.

Frequency of parent morph with supergenes (each color represents a different replicate)

Frequency of parent morph with supergenes (each color represents a different replicate)

Frequency of parents with supergenes in final generation
ParentFreq ParentW NonParentW
parent_supergene_1_summary.txt_1 0.851485 1.58372 0.546667
parent_supergene_1_summary.txt_2 0.830303 1.65693 0.642857
parent_supergene_1_summary.txt_3 0.859345 1.63004 0.739726
parent_supergene_1_summary.txt_4 0.844055 1.58661 0.612500
parent_supergene_2_summary.txt_1 0.632530 1.57778 0.327869
parent_supergene_2_summary.txt_2 0.544177 1.48339 0.374449
parent_supergene_2_summary.txt_3 0.587084 1.47000 0.265403
parent_supergene_2_summary.txt_4 0.610136 1.57827 0.480000
parent_supergene_3_summary.txt_1 0.540952 1.49296 0.311203
parent_supergene_3_summary.txt_2 0.562257 1.40484 0.297778
parent_supergene_3_summary.txt_3 0.595573 1.52365 0.393035
parent_supergene_3_summary.txt_4 0.489758 1.36882 0.277372
parent_supergene_4_summary.txt_1 0.540952 1.49296 0.311203
parent_supergene_4_summary.txt_2 0.562257 1.40484 0.297778
parent_supergene_4_summary.txt_3 0.595573 1.52365 0.393035
parent_supergene_4_summary.txt_4 0.489758 1.36882 0.277372
parent_supergene_5_summary.txt_1 0.832994 1.72861 0.548780
parent_supergene_5_summary.txt_2 0.848861 1.72927 0.547945
parent_supergene_5_summary.txt_3 0.854806 1.71531 0.535211
parent_supergene_5_summary.txt_4 0.863830 1.74877 0.671875

Variation was maintained in 20 of the 20. 0 of the 20 populations crashed, though. Of the 20 replicates, 20 reached an equilibrium by 10000 generations.

Courtship and Parental Traits

Females choose nests based on males’ courtship trait (they all only nest with courting males, and the female preference does not have a genetic basis and does not evolve), and then the survival of the nest depends on whether the courting male is also a parental male. If the chosen male is a parental male, the nest has a 90% chance of survival. Otherwise, it only has a 10% chance. Non-courters only reproduce through sneaking.

Frequency of the two morphs with linked QTLs (courter = green, parent = blue)

Frequency of the two morphs with linked QTLs (courter = green, parent = blue)

The different runs have different outcomes.

Let’s look at the morph frequencies.

Frequency of the 4 morphs in each rep with supergenes

Frequency of the 4 morphs in each rep with supergenes

In some of the runs the population crashed after few generations. This is obvious when looking at the the final frequencies in a table as well:

Frequency of morphs in final generation (supergenes)
Generation Pop PopSize NumMal NumFem NumProgeny ParentThresh ParentFreq ParentW NonParentW CourterThresh CourterFreq CourterW NonCourterW FreqNcNp FreqCNp FreqNcP FreqCP PrefThresh PrefFreq
parent-courter_supergene_1_summary.txt_1 11999 Pop0 940 463 477 1000 -1.305330 0.917927 1.898820 2.131580 0.0714242 0.917927 1.898820 2.13158 0.0820734 0.000000 0.0000000 0.9179270 NA NA
parent-courter_supergene_1_summary.txt_2 11999 Pop1 951 465 486 1000 -1.305330 0.888172 2.041160 1.615380 0.0714242 0.888172 2.041160 1.61538 0.1118280 0.000000 0.0000000 0.8881720 NA NA
parent-courter_supergene_1_summary.txt_3 11999 Pop2 942 473 469 1000 -1.305330 0.942918 1.838570 2.592590 0.0714242 0.942918 1.838570 2.59259 0.0570825 0.000000 0.0000000 0.9429180 NA NA
parent-courter_supergene_1_summary.txt_4 11999 Pop3 955 474 481 1000 -1.305330 0.938819 1.833710 2.517240 0.0714242 0.938819 1.833710 2.51724 0.0611814 0.000000 0.0000000 0.9388190 NA NA
parent-courter_supergene_2_summary.txt_1 10019 Pop0 986 507 479 1000 -1.345590 0.493097 0.200000 0.501946 -0.4086220 0.560158 0.630282 0.00000 0.0000000 0.506903 0.4398420 0.0532544 NA NA
parent-courter_supergene_2_summary.txt_2 10016 Pop1 62 29 33 85 -1.345590 0.241379 0.000000 0.000000 -0.4086220 0.758621 0.000000 0.00000 0.0000000 0.758621 0.2413790 0.0000000 NA NA
parent-courter_supergene_2_summary.txt_3 10018 Pop2 972 491 481 1000 -1.345590 0.531568 0.340996 0.426087 -0.4086220 0.539715 0.705660 0.00000 0.0000000 0.468432 0.4602850 0.0712831 NA NA
parent-courter_supergene_2_summary.txt_4 10018 Pop3 956 495 461 1000 -1.345590 0.535354 0.456604 0.352174 -0.4086220 0.557576 0.731884 0.00000 0.0000000 0.464646 0.4424240 0.0929293 NA NA
parent-courter_supergene_3_summary.txt_1 11999 Pop0 948 484 464 1000 -0.296238 0.946281 1.882100 1.923080 -0.9251540 0.946281 1.882100 1.92308 0.0537190 0.000000 0.0000000 0.9462810 NA NA
parent-courter_supergene_3_summary.txt_2 11999 Pop1 953 470 483 1000 -0.296238 0.963830 1.874170 2.529410 -0.9251540 0.963830 1.874170 2.52941 0.0361702 0.000000 0.0000000 0.9638300 NA NA
parent-courter_supergene_3_summary.txt_3 11999 Pop2 957 491 466 1000 -0.296238 0.892057 1.892690 1.358490 -0.9251540 0.892057 1.892690 1.35849 0.1079430 0.000000 0.0000000 0.8920570 NA NA
parent-courter_supergene_3_summary.txt_4 11999 Pop3 992 494 498 1000 -0.296238 0.898785 1.882880 1.100000 -0.9251540 0.898785 1.882880 1.10000 0.1012150 0.000000 0.0000000 0.8987850 NA NA
parent-courter_supergene_4_summary.txt_1 11999 Pop0 948 484 464 1000 -0.296238 0.946281 1.882100 1.923080 -0.9251540 0.946281 1.882100 1.92308 0.0537190 0.000000 0.0000000 0.9462810 NA NA
parent-courter_supergene_4_summary.txt_2 11999 Pop1 953 470 483 1000 -0.296238 0.963830 1.874170 2.529410 -0.9251540 0.963830 1.874170 2.52941 0.0361702 0.000000 0.0000000 0.9638300 NA NA
parent-courter_supergene_4_summary.txt_3 11999 Pop2 957 491 466 1000 -0.296238 0.892057 1.892690 1.358490 -0.9251540 0.892057 1.892690 1.35849 0.1079430 0.000000 0.0000000 0.8920570 NA NA
parent-courter_supergene_4_summary.txt_4 11999 Pop3 992 494 498 1000 -0.296238 0.898785 1.882880 1.100000 -0.9251540 0.898785 1.882880 1.10000 0.1012150 0.000000 0.0000000 0.8987850 NA NA
parent-courter_supergene_5_summary.txt_1 11999 Pop0 959 476 483 1000 -0.836030 0.924370 1.870450 1.888890 0.4151430 0.924370 1.870450 1.88889 0.0756303 0.000000 0.0000000 0.9243700 NA NA
parent-courter_supergene_5_summary.txt_2 11999 Pop1 971 487 484 1000 -0.836030 0.915811 1.836320 1.707320 0.4151430 0.915811 1.836320 1.70732 0.0841889 0.000000 0.0000000 0.9158110 NA NA
parent-courter_supergene_5_summary.txt_3 11999 Pop2 992 491 501 1000 -0.836030 0.918534 1.871400 1.575000 0.4151430 0.916497 1.875560 1.53659 0.0814664 0.000000 0.0020367 0.9164970 NA NA
parent-courter_supergene_5_summary.txt_4 11999 Pop3 951 471 480 1000 -0.836030 0.921444 1.963130 1.837840 0.4151430 0.921444 1.963130 1.83784 0.0785563 0.000000 0.0000000 0.9214440 NA NA

Multiple morphs are maintained in 20 of the 20 replicates, and those morphs contain either a parent or a courter. However, 0 of those reps with variation actually crashed.